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hmgu-itg / peakplotter

A tool to find and annotate signals in next-generation association studies
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Na bug #19

Closed singharchit97 closed 2 years ago

singharchit97 commented 2 years ago

Fixed the NA bug issue in the summary stats input file (when the pvalue/ any other extra column column has NA).

youngchanpark commented 2 years ago

Hey @singharchit97,

I ran pytest and the test_read_asoc_for_NA_values_in_extra_column test is failing.

A few minor edits to the test:

  1. See the parameter list for plotpeaks.read_assoc. You've got one extra (hint hint) parameter there you don't need.
  2. Minor typo in the MAF column of the input example data (or the expected dataframe, whichever you want to fix)
  3. The datatype of the extra column between the input and expected dataframe needs to match (see the error message once you ran pytest after fixing the above two problems)

The number 3 you may need to think about whether to modify the test or the plotpeaks.read_assoc function itself, depending on what we expect.